Just checking. Are you able to get this web object working within Presenter the normal way ? ie. without trying to get rid of the borders. Looks like your web object has built in code to remove the 'Click to activate Flash' message (activating active content) you get sometimes with embedded Flash. Maybe that is interfering. I will investigate.
What sort of webobject is it? Camtasia uses another non-Adobe solution to the active control problem, which is actually a 'open to all' solution called SWFObject available
here. I have just corrected a Flash web object using the no-borders solution I mentioned plus the SWFObject solution for the activating active content issue. You can see it
here. The web object is the 'Arrow Training'.
One option (maybe) would be to use the SWFObject solution to reference your swf files.
PS. Gary, if you could give me a dummy example of your web object, then I would have a go myself.